Should I use a 0-based or 1-based coordinate system when creating a custom annotation track? E.g. to indicate a single nucleotide, should the posstart and posend column be identical (1-based system) or should they differ by one (0-based system)?

1 answer

Currently in our analysis software SVS 8 (soon to be in GenomeBrowse 2.0!), there are three options for how the coordinates can be classified. The differences between these options result in different widths of the created features.

0-Based Interval (Half-open Interval): Here you have both a Start and a Stop position field and the width of the created feature would be Stop - Start, and the smallest start can be zero.

1-Based Interval (Indexed Interval): Here you have both a Start and a Stop position field and the width of the created feature would be Stop - Start + 1, and the smallest start can be one.

Position (1bp width): Here you have a single position field and it assumed that the width of every feature would be 1bp.

You can use any of these options to create a single nucleotide track, the simplest is the Position option where the position column selected should represent the location of the nucleotide on the chromosome.

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